Statistical mechanics of nucleosome ordering by chromatin structure-induced two-body interactions

One-dimensional arrays of nucleosomes (DNA-bound histone octamers separated by stretches of linker DNA) fold into higher-order chromatin structures which ultimately make up eukaryotic chromosomes. Chromatin structure formation leads to 10-11 base pair (bp) discretization of linker lengths caused by the smaller free energy cost of packaging nucleosomes into a regular chromatin fiber if their rotational setting (defined by DNA helical twist) is conserved. We describe nucleosome positions along the fiber using a thermodynamic model of finite-size particles with effective two-body interactions, subject to an arbitrary external potential. We infer both one-body and two-body energies from readily available large-scale maps of nucleosome positions. We show that two-body forces play a leading role in establishing well-known 10-11 bp genome-wide periodicity of nucleosome occupancies. They also explain nucleosome ordering over transcribed regions observed in both in vitro and in vivo high-throughput experiments.Comment: 4 pages, 3 figure

Lagrangian Pairs and Lagrangian Orthogonal Matroids

Represented Coxeter matroids of types $C_n$ and $D_n$, that is, symplectic and orthogonal matroids arising from totally isotropic subspaces of symplectic or (even-dimensional) orthogonal spaces, may also be represented in buildings of type $C_n$ and $D_n$, respectively. Indeed, the particular buildings involved are those arising from the flags or oriflammes, respectively, of totally isotropic subspaces. There are also buildings of type $B_n$ arising from flags of totally isotropic subspaces in odd-dimensional orthogonal space. Coxeter matroids of type $B_n$ are the same as those of type $C_n$ (since they depend only upon the reflection group, not the root system). However, buildings of type $B_n$ are distinct from those of the other types. The matroids representable in odd dimensional orthogonal space (and therefore in the building of type $B_n$) turn out to be a special case of symplectic (flag) matroids, those whose top component, or Lagrangian matroid, is a union of two Lagrangian orthogonal matroids. These two matroids are called a Lagrangian pair, and they are the combinatorial manifestation of the ``fork'' at the top of an oriflamme (or of the fork at the end of the Coxeter diagram of $D_n$). Here we give a number of equivalent characterizations of Lagrangian pairs, and prove some rather strong properties of them.Comment: Requires amssymb.sty; 12 pages, 2 LaTeX figure

Dynamical mechanism for ultra-light scalar Dark Matter

Assuming a double-well bare potential for a self-interacting scalar field, with the Higgs vacuum expectation value, it is shown that non-perturbative quantum corrections naturally lead to ultra-light particles of mass $\simeq10^{-23}$eV, if these non-perturbative effects occur at a time consistent with the Electroweak phase transition. This mechanism could be relevant in the context of Bose Einstein Condensate studies for the description of cold Dark Matter. Given the numerical consistency with the Electroweak transition, an interaction potential for Higgs and Dark Matter fields is proposed, where spontaneous symmetry breaking for the Higgs field leads to the generation of ultra-light particles, in addition to the usual Higgs mechanism. This model also naturally leads to extremely weak interactions between the Higgs and Dark Matter particles.Comment: 12 pages, includes the derivation of the effective potential suppressed by the volum

Lagrangian Matroids: Representations of Type BnB_n

We introduce the concept of orientation for Lagrangian matroids represented in the flag variety of maximal isotropic subspaces of dimension N in the real vector space of dimension 2N+1. The paper continues the study started in math.CO/0209100.Comment: Requires amssymb.sty; 17 page